Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of similar to 2900 cell divisions yielded a base-substitution mutation rate of 1.22 x 10(-10) per site per generation or 4 x 10(-4) per genome per generation, which is significantly lower than the consensus value (2.5-4.6 x 10(-3)) of mesothermophilic (similar to 15-40 degrees C) and neutrophilic (pH 6-8) prokaryotic organisms. However, the insertion-deletion rate (0.43 x 10(-10) per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.